def test_that_non_matching_workspaces_are_detected(self):
# Arrange
front_name = "front"
rear_name = "rear"
result_name = "result"
x1 = [1,2,3]
e1 = [1,1]
y1 = [2,2]
dx1 = [1.,2.,3.]
x2 = [1,2,3,4]
e2 = [1,1, 1]
y2 = [2,2, 2]
dx2 = [1.,2.,3.,4.]
provide_workspace_with_x_errors(front_name, True, 1, x1, y1, e1, dx1)
provide_workspace_with_x_errors(rear_name, True, 1, x2, y2, e2, dx2)
provide_workspace_with_x_errors(result_name, False, 1)
front = mtd[front_name]
rear = mtd[rear_name]
result = mtd[result_name]
scale = 2.
# Act
su.correct_q_resolution_for_merged(front, rear,result, scale)
# Assert
self.assertFalse(result.hasDx(0))
# Clean up
DeleteWorkspace(front)
DeleteWorkspace(rear)
DeleteWorkspace(result)
def test_monitors_are_renamed_correctly(self):
#Arrange
ws_1 = CreateSampleWorkspace()
ws_2 = CreateSampleWorkspace()
ws_3 = CreateSampleWorkspace()
ws_mon_1 = CreateSampleWorkspace()
ws_mon_2 = CreateSampleWorkspace()
ws_mon_3 = CreateSampleWorkspace()
ws_group = GroupWorkspaces(InputWorkspaces=[ws_1, ws_2, ws_3])
ws_mon_group = GroupWorkspaces(InputWorkspaces=[ws_mon_1, ws_mon_2, ws_mon_3])
# Act
su.rename_monitors_for_multiperiod_event_data(ws_mon_group, ws_group, self.monitor_appendix)
# Assert
self.assertTrue(ws_mon_1.name() == ws_1.name() + self.monitor_appendix, "Monitors should be renamed to xxxx_monitors")
self.assertTrue(ws_mon_2.name() == ws_2.name() + self.monitor_appendix, "Monitors should be renamed to xxxx_monitors")
self.assertTrue(ws_mon_3.name() == ws_3.name() + self.monitor_appendix, "Monitors should be renamed to xxxx_monitors")
# Clean up
for element in mtd.getObjectNames():
if element in mtd:
DeleteWorkspace(element)
def test_removes_zero_errors_correctly(self):
# Arrange
ws_name = 'test'
type ='Histogram'
self._setup_workspace(ws_name, type)
ws = mtd[ws_name]
# Act and Assert
errors = ws.dataE
self.assertTrue(errors(0)[0] == 0.0)
self.assertTrue(errors(1)[0] != 0.0)
self.assertTrue(errors(2)[0] == 0.0)
self.assertTrue(errors(3)[0] != 0.0)
su.remove_zero_errors_from_workspace(ws)
self.assertTrue(errors(0)[0] == su.ZERO_ERROR_DEFAULT)
self.assertTrue(errors(1)[0] != 0.0)
self.assertTrue(errors(1)[0] != su.ZERO_ERROR_DEFAULT)
self.assertTrue(errors(2)[0] == su.ZERO_ERROR_DEFAULT)
self.assertTrue(errors(3)[0] != 0.0)
self.assertTrue(errors(3)[0] != su.ZERO_ERROR_DEFAULT)
self._removeWorkspace(ws_name)
self.assertTrue(not ws_name in mtd)
def _match_IDF(self, run):
'''
Compares the IDF in the stored instrument with the IDF in the workspace.
If they are the same all is well. If they diff, then load the adequate
user file.
@param run: name of the run for which the file is to be extracted
'''
# We need the instrument name and the measurement time to determine
# the IDF
measurement_time = None
instrument_name = self.get_instrument_name()
# We need to be able to handle file-based and workspace-based queries
# If we have a workspace we look at the end time, else we
# need a sophisticated extraction mechanism
if isinstance(run, Workspace):
ws = None
if isinstance(run, WorkspaceGroup):
# Just look at the first element in a workspace group
ws = run[0]
else:
ws = run
measurement_time = str(ws.getRun().endTime()).strip()
else:
if run is None or run == "":
return
measurement_time = su.get_measurement_time_from_file(run)
# Get the path to the instrument definition file
idf_path_workspace = ExperimentInfo.getInstrumentFilename(instrument_name, measurement_time)
idf_path_workspace = os.path.normpath(idf_path_workspace)
# Get the idf from the reducer
idf_path_reducer = self.get_idf_file_path()
idf_path_reducer = os.path.normpath(idf_path_reducer)
# Now check if both idf paths and underlying files. If they are, then don't do anything
# else switch the underlying instrument
if idf_path_reducer == idf_path_workspace and su.are_two_files_identical(idf_path_reducer, idf_path_reducer):
return
else:
logger.notice("Updating the IDF of the Reducer. Switching from " +
str(idf_path_reducer) + " to " + str(idf_path_workspace))
idf_path = os.path.basename(idf_path_workspace)
instrument = self._get_correct_instrument(instrument_name, idf_path)
# Get detector of the old instrument
old_instrument = self.get_instrument()
old_detector_selection = old_instrument.get_detector_selection()
if instrument is not None:
self.set_instrument(instrument)
# We need to update the instrument, by reloading the user file.
# This is pretty bad, but looking at the reducer architecture this
# seems to be the only reasonable way to do this.
self.user_settings.execute(self)
# Now we set the correct detector, this is also being done in the GUI
self.get_instrument().setDetector(old_detector_selection)
def set_run(self, run, reload, period, reducer):
super(Can, self).set_run(run, reload, period, reducer)
# currently, no slices will be applied to Can #8535
for period in reversed(range(self.loader.periods_in_file)):
self.loader.move2ws(period)
name = self.loader.wksp_name
if su.isEventWorkspace(name):
su.fromEvent2Histogram(mtd[name], self.get_monitor())
def set_run(self, run, reload, period, reducer):
super(Can, self).set_run(run, reload, period, reducer)
# currently, no slices will be applied to Can #8535
for period in reversed(range(self.loader.periods_in_file)):
self.loader.move2ws(period)
name = self.loader.wksp_name
if su.isEventWorkspace(name):
su.fromEvent2Histogram(mtd[name], self.get_monitor())
def delete_cloned_workspaces(save_names_dict):
"""
If there are cloned workspaces in the worksapce map, then they are deleted
@param save_names_dict: a workspace name map
"""
to_delete =[]
for key in save_names_dict:
if key != save_names_dict[key]:
to_delete.append(save_names_dict[key])
for element in to_delete:
su.delete_zero_error_free_workspace(input_workspace_name = element)
def delete_cloned_workspaces(save_names_dict):
"""
If there are cloned workspaces in the worksapce map, then they are deleted
@param save_names_dict: a workspace name map
"""
to_delete =[]
for key in save_names_dict:
if key != save_names_dict[key]:
to_delete.append(save_names_dict[key])
for element in to_delete:
su.delete_zero_error_free_workspace(input_workspace_name = element)
def test_converts_true_to_float_when_float(self):
# Arrange
input = 3.8
# Act
result = su.is_convertible_to_float(input)
# Assert
self.assertTrue(result)
def test_load_valid_added_event_data_and_monitor_file_produces_group_ws(self):
# Arrange
names = ['event_data', 'monitor']
file_names = self._prepare_workspaces(names = names)
self._cleanup_workspaces(names = names)
# Act
group_ws_name = 'g_ws'
output_group_file_name = su.bundle_added_event_data_as_group(file_names[0], file_names[1])
Load(Filename = output_group_file_name, OutputWorkspace = group_ws_name)
group_ws = mtd[group_ws_name]
# Assert
self.assertTrue(isinstance(group_ws, WorkspaceGroup))
self.assertEqual(group_ws.size(), 2)
self.assertTrue(os.path.exists(file_names[0])) # File for group workspace exists
self.assertFalse(os.path.exists(file_names[1])) # File for monitors is deleted
# Clean up
ws_names_to_delete = []
for ws_name in mtd.getObjectNames():
if ws_name != group_ws_name:
ws_names_to_delete.append(str(ws_name))
self._cleanup_workspaces(names = ws_names_to_delete)
if os.path.exists(file_names[0]):
os.remove(file_names[0])
def test_that_error_is_transferred(self):
# Arrange
x1 = [1,2,3,4,5,6,7,8,9]
x2 = [1,2,3,4,5,6,7,8,9]
y1 = [2,2,2,2,2,2,2,2]
y2 = [2,2,2,2,2,2,2,2]
e1 = [1,1,1,1,1,1,1,1]
e2 = [2,2,2,2,2,2,2,2]
front, rear = self._createWorkspace(x1,y1, e1, x2, y2, e2)
x_min = 3
x_max = 7
# Act
f_return, r_return = su.get_error_corrected_front_and_rear_data_sets(front, rear,x_min, x_max)
# Assert
self.assertEqual(5, len(f_return.dataX(0)))
self.assertEqual(5, len(r_return.dataX(0)))
expected_errors_in_rear = [np.sqrt(5),np.sqrt(5),np.sqrt(5),np.sqrt(5)]
self.assertTrue(expected_errors_in_rear[0] == r_return.dataE(0)[0])
self.assertTrue(expected_errors_in_rear[1] == r_return.dataE(0)[1])
self.assertTrue(expected_errors_in_rear[2] == r_return.dataE(0)[2])
self.assertTrue(expected_errors_in_rear[3] == r_return.dataE(0)[3])
# Clean up
DeleteWorkspace(front)
DeleteWorkspace(rear)
def test_convertible_true_to_float_when_convertible_string(self):
# Arrange
input = "4.78"
# Act
result = su.is_convertible_to_float(input)
# Assert
self.assertTrue(result)
def test__converts_false_to_integer_when_non_convertible_string(self):
# Arrange
input = '34_gt'
# Act
result = su.is_convertible_to_int(input)
# Assert
self.assertFalse(result)
def test_converts_false_to_float_when_convertible_string(self):
# Arrange
input = "4.78_tg"
# Act
result = su.is_convertible_to_float(input)
# Assert
self.assertFalse(result)
def test_finds_invalid_xml_file_list(self):
# Arrange
input = ["test1.xml", "test2.ccl", "test3.xml"]
# Act
result =su.is_valid_xml_file_list(input)
# Assert
self.assertFalse(result)
def test_converts_true_to_integer_when_convertible_string(self):
# Arrange
input = '34'
# Act
result = su.is_convertible_to_int(input)
# Assert
self.assertTrue(result)
def test_finds_empty_list(self):
# Arrange
input = []
# Act
result = su.is_valid_xml_file_list(input)
# Assert
self.assertFalse(result)
def _do_test(self, file_name, expected_time):
exists, full_path = get_full_path_SANS_system_test(file_name)
if exists:
measurement_time = su.get_measurement_time_from_file(full_path)
self.assertEqual(measurement_time, expected_time)
else:
print("Missing data files. Path to system test data needs to be set.")
self.assertTrue(False)
def do_test_extraction(self, event_name, monitor_name):
out_ws_name = 'out_group'
event_name_expect = out_ws_name
monitor_name_expect = out_ws_name + self._appendix
provide_group_workspace_for_added_event_data(event_ws_name = event_name, monitor_ws_name = monitor_name, out_ws_name = out_ws_name)
out_ws_group = mtd[out_ws_name]
# Act
su.extract_child_ws_for_added_eventdata(out_ws_group, self._appendix)
# Assert
self.assertTrue(event_name_expect in mtd)
self.assertTrue(monitor_name_expect in mtd)
DeleteWorkspace(event_name_expect)
DeleteWorkspace(monitor_name_expect)
def test_converts_from_string_to_list(self):
# Arrange
input = "test1.xml, test2.xml, test3.xml"
# Act
result = su.convert_to_string_list(input)
# Assert
expected = "['test1.xml','test2.xml','test3.xml']"
self.assertEqual(expected, result)
def test_converts_from_list_to_string(self):
# Arrange
input = ["test1.xml", "test2.xml", "test3.xml"]
# Act
result = su.convert_from_string_list(input)
# Assert
expected = "test1.xml,test2.xml,test3.xml"
self.assertEqual(expected, result)
def setUserFileInBatchMode(new_user_file, current_user_file,
original_user_file, original_settings,
original_prop_man_settings):
"""
Loads a specified user file. The file is loaded if
new_user_file is different from current_user_file. Else we just
keep the user file loaded. If the new_user_file is empty then we default to
original_user_file.
@param new_user_file: The new user file. Note that this can be merely the filename (+ extension)
@param current_user_file: The currently loaded user file
@param original_user_file: The originally loaded user file. This is used as a default
@param original_settings: The original reducer
@param original_prop_man_settings: Original properties settings
"""
user_file_to_set = ""
if new_user_file == '':
user_file_to_set = original_user_file
else:
# Try to find the user file in the default paths
if not os.path.isfile(new_user_file):
# Find the user file in the Mantid path. we make sure that the user file has a txt extension.
user_file_names_with_extension = su.get_user_file_name_options_with_txt_extension(
new_user_file)
for user_file_name_with_extension in user_file_names_with_extension:
user_file = FileFinder.getFullPath(
user_file_name_with_extension)
if user_file:
break
if not os.path.isfile(user_file):
message = "Error could not find specified user file {0}"\
.format(new_user_file)
raise RuntimeError(message)
else:
user_file_to_set = user_file
else:
user_file_to_set = new_user_file
# Set the user file in the reducer and load the user file
if os.path.normpath(user_file_to_set) != os.path.normpath(
current_user_file):
# Need to setup a clean reducer. If we are dealing with the original user file,
# then we should take gui changes into account, ie reset to the original reducer
if user_file_to_set == original_user_file:
ReductionSingleton().replace(copy.deepcopy(original_settings))
ReductionSingleton().settings = original_prop_man_settings.clone(
REDUCTION_SETTINGS_OBJ_NAME)
else:
instrument = copy.deepcopy(ReductionSingleton().get_instrument())
output_type = ReductionSingleton().to_Q.output_type
ReductionSingleton().clean(isis_reducer.ISISReducer)
ReductionSingleton().set_instrument(instrument)
ReductionSingleton().user_settings = UserFile(user_file_to_set)
ReductionSingleton().to_Q.output_type = output_type
ReductionSingleton().user_settings.execute(ReductionSingleton())
current_user_file = user_file_to_set
return current_user_file
def test_that_deletion_of_non_existent_ws_creates_error_message(self):
# Arrange
ws_name = 'ws'
# Act
message, complete = su.delete_zero_error_free_workspace(input_workspace_name = ws_name)
# Assert
message.strip()
self.assertTrue(message)
self.assertTrue(not complete)
def _create_quadrant(self, setup, reduced_ws, quadrant, xcentre, ycentre, r_min, r_max, suffix):
out_ws = quadrant+suffix
# Need to create a copy because we're going to mask 3/4 out and that's a one-way trip
CloneWorkspace(InputWorkspace=reduced_ws,OutputWorkspace= out_ws)
objxml = SANSUtility.QuadrantXML([0, 0, 0.0], r_min, r_max, quadrant)
# Mask out everything outside the quadrant of interest
MaskDetectorsInShape(Workspace=out_ws,ShapeXML= objxml)
setup.to_Q.execute(setup, out_ws)
def test_error_is_ignored_for_more_than_one_spectrum(self):
# Arrange
orig_name = "orig"
can_name = "can"
result_name = "result"
provide_workspace_with_x_errors(orig_name, True, 2)
provide_workspace_with_x_errors(can_name, True, 2)
provide_workspace_with_x_errors(result_name, False, 2)
orig = mtd[orig_name]
can = mtd[can_name]
result = mtd[result_name]
# Act
su.correct_q_resolution_for_can(orig, can, result)
# Assert
self.assertFalse(result.hasDx(0))
# Clean up
DeleteWorkspace(orig)
DeleteWorkspace(can)
DeleteWorkspace(result)
def test_error_is_not_passed_on_when_did_not_exist_beforehand(self):
# Arrange
orig_name = "orig"
can_name = "can"
result_name = "result"
provide_workspace_with_x_errors(orig_name, False, 1)
provide_workspace_with_x_errors(can_name, False, 1)
provide_workspace_with_x_errors(result_name, False, 1)
orig = mtd[orig_name]
can = mtd[can_name]
result = mtd[result_name]
# Act
su.correct_q_resolution_for_can(orig, can, result)
# Assert
self.assertFalse(result.hasDx(0))
# Clean up
DeleteWorkspace(orig)
DeleteWorkspace(can)
DeleteWorkspace(result)
def post_process(self):
# Store the mask file within the final workspace so that it is saved to the CanSAS file
if self.user_settings is None:
user_file = 'None'
else:
user_file = self.user_settings.filename
AddSampleLog(Workspace=self.output_wksp,
LogName="UserFile",
LogText=user_file)
# get the value of __transmission_sample from the transmission_calculator if it has
if (not self.get_can()) and self.transmission_calculator.output_wksp:
# it updates only if there was not can, because, when there is can, the __transmission_sample
# is already correct and transmission_calculator.output_wksp points to the can transmission
self.__transmission_sample = self.transmission_calculator.output_wksp
# The reducer itself sometimes will be reset, and the users of the singleton
# not always will have access to its settings. So, we will add the transmission workspaces
# to the SampleLog, to be connected to the workspace, and be available outside. These values
# are current being used for saving CanSAS (ticket #6929)
if self.__transmission_sample:
unfitted_transmission_workspace_name = su.get_unfitted_transmission_workspace_name(
self.__transmission_sample)
AddSampleLog(Workspace=self.output_wksp,
LogName="Transmission",
LogText=unfitted_transmission_workspace_name)
if self.__transmission_can:
unfitted_transmission_workspace_name = su.get_unfitted_transmission_workspace_name(
self.__transmission_can)
AddSampleLog(Workspace=self.output_wksp,
LogName="TransmissionCan",
LogText=unfitted_transmission_workspace_name)
# clean these values for subsequent executions
self.__transmission_sample = ""
self.__transmission_can = ""
for role in list(self._temporys.keys()):
try:
DeleteWorkspace(Workspace=self._temporys[role])
except (Exception, Warning):
# if cleaning up isn't possible there is probably nothing we can do
pass
def _get_idf_path_for_workspace(self, filename, instrument_name):
exists, full_path = get_full_path_SANS_system_test(filename)
idf_path_workspace = None
if exists:
measurement_time = su.get_measurement_time_from_file(full_path)
idf_path_workspace = ExperimentInfo.getInstrumentFilename(instrument_name, measurement_time)
else:
print("Missing data files. Path to system test data needs to be set.")
self.assertTrue(False)
return idf_path_workspace
def test_that_non_existent_ws_creates_error_message(self):
# Arrange
ws_name = 'original'
ws_clone_name = 'clone'
# Act
message, complete = su.create_zero_error_free_workspace(input_workspace_name = ws_name, output_workspace_name = ws_clone_name)
# Assert
message.strip()
self.assertTrue(message)
self.assertTrue(not complete)
def test_that_deletion_of_extent_ws_is_successful(self):
# Arrange
ws_name = 'ws'
self._setup_workspace(ws_name, 'Histogram')
# Act + Assert
self.assertTrue(ws_name in mtd)
message, complete = su.delete_zero_error_free_workspace(input_workspace_name = ws_name)
message.strip()
self.assertTrue(not message)
self.assertTrue(complete)
self.assertTrue(not ws_name in mtd)
def test_error_is_ignored_when_only_one_input_has_dx(self):
# Arrange
front_name = "front"
rear_name = "rear"
result_name = "result"
provide_workspace_with_x_errors(front_name, True, 1)
provide_workspace_with_x_errors(rear_name, False, 1)
provide_workspace_with_x_errors(result_name, False, 1)
front = mtd[front_name]
rear = mtd[rear_name]
result = mtd[result_name]
scale = 2.
# Act
su.correct_q_resolution_for_merged(front, rear,result, scale)
# Assert
self.assertFalse(result.hasDx(0))
# Clean up
DeleteWorkspace(front)
DeleteWorkspace(rear)
DeleteWorkspace(result)
def test_get_masked_det_ids(self):
ws = CreateSampleWorkspace("Histogram", "Multiple Peaks")
MaskDetectors(Workspace=ws, DetectorList=[100, 102, 104])
masked_det_ids = list(su.get_masked_det_ids(ws))
self.assertTrue(100 in masked_det_ids)
self.assertTrue(102 in masked_det_ids)
self.assertTrue(104 in masked_det_ids)
self.assertEquals(len(masked_det_ids), 3)
def test_parse_strings(self):
inputs = { '1-2':[[1,2]], # single period syntax min < x < max
'1.3-5.6':[[1.3,5.6]], # float
'1-2,3-4':[[1,2],[3,4]],# more than one slice
'>1':[[1, -1]], # just lower bound
'<5':[[-1, 5]], # just upper bound
'<5,8-9': [[-1, 5], [8,9]],
'1:2:5': [[1,3], [3,5]] # sintax: start, step, stop
}
for (k, v) in inputs.items():
self.checkValues(su.sliceParser(k),v)
def setUserFileInBatchMode(new_user_file, current_user_file, original_user_file, original_settings, original_prop_man_settings):
"""
Loads a specified user file. The file is loaded if
new_user_file is different from current_user_file. Else we just
keep the user file loaded. If the new_user_file is empty then we default to
original_user_file.
@param new_user_file: The new user file. Note that this can be merely the filename (+ extension)
@param current_user_file: The currently loaded user file
@param original_user_file: The originally loaded user file. This is used as a default
@param original_settings: The original reducer
@param original_prop_man_settings: Original properties settings
"""
user_file_to_set = ""
if new_user_file == '':
user_file_to_set = original_user_file
else:
# Try to find the user file in the default paths
if not os.path.isfile(new_user_file):
# Find the user file in the Mantid path. we make sure that the user file has a txt extension.
user_file_names_with_extension = su.get_user_file_name_options_with_txt_extension(new_user_file)
for user_file_name_with_extension in user_file_names_with_extension:
user_file = FileFinder.getFullPath(user_file_name_with_extension)
if user_file:
break
if not os.path.isfile(user_file):
message = "Error could not find specified user file {0}"\
.format(new_user_file)
raise RuntimeError(message)
else:
user_file_to_set = user_file
else:
user_file_to_set = new_user_file
# Set the user file in the reducer and load the user file
if os.path.normpath(user_file_to_set) != os.path.normpath(current_user_file):
# Need to setup a clean reducer. If we are dealing with the original user file,
# then we should take gui changes into account, ie reset to the original reducer
if user_file_to_set == original_user_file:
ReductionSingleton().replace(copy.deepcopy(original_settings))
ReductionSingleton().settings = original_prop_man_settings.clone(REDUCTION_SETTINGS_OBJ_NAME)
else:
instrument = copy.deepcopy(ReductionSingleton().get_instrument())
output_type = ReductionSingleton().to_Q.output_type
ReductionSingleton().clean(isis_reducer.ISISReducer)
ReductionSingleton().set_instrument(instrument)
ReductionSingleton().user_settings = UserFile(user_file_to_set)
ReductionSingleton().to_Q.output_type = output_type
ReductionSingleton().user_settings.execute(ReductionSingleton())
current_user_file = user_file_to_set
return current_user_file
def test_non_Q1D_and_Qxy_history_is_not_valid_and_produces_error_message(self):
# Arrange
ws_name = 'ws'
self._setup_workspace(ws_name, 'Histogram')
# Act
message, complete = su.is_valid_ws_for_removing_zero_errors(input_workspace_name = ws_name)
# Assert
message.strip()
self.assertTrue(message)
self.assertTrue(not complete)
self._removeWorkspace(ws_name)
self.assertTrue(not ws_name in mtd)
def test_parse_strings(self):
inputs = {
'1-2': [[1, 2]], # single period syntax min < x < max
'1.3-5.6': [[1.3, 5.6]], # float
'1-2,3-4': [[1, 2], [3, 4]], # more than one slice
'>1': [[1, -1]], # just lower bound
'<5': [[-1, 5]], # just upper bound
'<5,8-9': [[-1, 5], [8, 9]],
'1:2:5': [[1, 3], [3, 5]] # sintax: start, step, stop
}
for (k, v) in inputs.items():
self.checkValues(su.sliceParser(k), v)
def get_mapped_workspaces(save_names, save_as_zero_error_free):
"""
Get a workspace name map, which maps from the original
workspace to a zero-error-free cloned workspace if
save_as_zero_error_free is checked otherwise the
workspaces are mapped to themselves.
@param save_names: a list of workspace names
@param save_as_zero_error_free : if the user wants the zero-errors removed
@returns a map of workspaces
"""
workspace_dictionary = {}
for name in save_names:
if save_as_zero_error_free:
cloned_name = name + '_cloned_temp'
dummy_message, complete = su.create_zero_error_free_workspace(input_workspace_name = name, output_workspace_name = cloned_name)
if complete:
workspace_dictionary[name] = cloned_name
else:
workspace_dictionary[name] = name
else:
workspace_dictionary[name] = name
return workspace_dictionary
def BatchReduce(
filename,
format,
plotresults=False,
saveAlgs={'SaveRKH': 'txt'},
verbose=False, # noqa: C901
centreit=False,
reducer=None,
combineDet=None,
save_as_zero_error_free=False):
"""
@param filename: the CSV file with the list of runs to analyse
@param format: type of file to load, nxs for Nexus, etc.
@param plotresults: if true and this function is run from Mantidplot a graph will be created for the results of each reduction
@param saveAlgs: this named algorithm will be passed the name of the results workspace and filename (default = 'SaveRKH').
Pass a tuple of strings to save to multiple file formats
@param verbose: set to true to write more information to the log (default=False)
@param centreit: do centre finding (default=False)
@param reducer: if to use the command line (default) or GUI reducer object
@param combineDet: that will be forward to WavRangeReduction (rear, front, both, merged, None)
@param save_as_zero_error_free: Should the reduced workspaces contain zero errors or not
@return final_setings: A dictionary with some values of the Reduction - Right Now:(scale, shift)
"""
if not format.startswith('.'):
format = '.' + format
# Read CSV file and store information in runinfo using format IN_FORMAT
file_handle = open(filename, 'r')
runinfo = []
for line in file_handle:
# See how many pieces of information have been provided;
# brackets delineate the field separator (nothing for space-delimited, ',' for comma-seperated)
parts = line.rstrip().split(',')
if addRunToStore(parts, runinfo) > 0:
issueWarning('Incorrect structure detected in input file "' +
filename + '" at line \n"' + line +
'"\nEntry skipped\n')
file_handle.close()
if reducer:
ReductionSingleton().replace(reducer)
ins_name = ReductionSingleton().instrument.name()
# is used for SaveCanSAS1D go give the detectors names
detnames = ', '.join(ReductionSingleton().instrument.listDetectors())
# LARMOR has just one detector, but, it defines two because ISISInstrument is defined as two banks! #8395
if ins_name == 'LARMOR':
detnames = ReductionSingleton().instrument.cur_detector().name()
scale_shift = {'scale': 1.0000, 'shift': 0.0000}
#first copy the user settings in case running the reductionsteps can change it
settings = copy.deepcopy(ReductionSingleton().reference())
prop_man_settings = ReductionSingleton().settings.clone("TEMP_SETTINGS")
# Make a note of the original user file, as we want to set it
original_user_file = ReductionSingleton().user_settings.filename
current_user_file = original_user_file
# Store the original combineDet which was set either by the input. this should be used whenever we are using the
# original user file
original_combine_det = combineDet
# Now loop over all the lines and do a reduction (hopefully) for each
for run in runinfo:
# Set the user file, if it is required
try:
current_user_file = setUserFileInBatchMode(
new_user_file=run['user_file'],
current_user_file=current_user_file,
original_user_file=original_user_file,
original_settings=settings,
original_prop_man_settings=prop_man_settings)
if current_user_file == original_user_file:
combineDet = original_combine_det
else:
# When we set a new user file, that means that the combineDet feature could be invalid,
# ie if the detector under investigation changed in the user file. We need to change this
# here too. But only if it is not None.
if combineDet is not None:
new_combineDet = ReductionSingleton(
).instrument.get_detector_selection()
combineDet = su.get_correct_combinDet_setting(
ins_name, new_combineDet)
except (RuntimeError, ValueError) as e:
raise RuntimeError(
"Error in Batchmode user files: Could not reset the specified user file {0}. More info: {1}"
.format(str(run['user_file']), str(e)))
local_settings = copy.deepcopy(ReductionSingleton().reference())
local_prop_man_settings = ReductionSingleton().settings.clone(
"TEMP_SETTINGS")
raw_workspaces = []
geometry_properties = {}
try:
# Load in the sample runs specified in the csv file
raw_workspaces.append(read_run(run, 'sample_sans', format))
#Transmission runs to be applied to the sample
raw_workspaces += read_trans_runs(run, 'sample', format)
# Can run
raw_workspaces.append(read_run(run, 'can_sans', format))
#Transmission runs for the can
raw_workspaces += read_trans_runs(run, 'can', format)
if centreit == 1:
if verbose == 1:
FindBeamCentre(50., 170., 12)
try:
geometry_properties = get_geometry_properties(
ReductionSingleton())
except RuntimeError as e:
message = "Could not extract geometry properties from the reducer: {0}".format(
str(e))
sanslog.warning(message)
# WavRangeReduction runs the reduction for the specified
# wavelength range where the final argument can either be
# DefaultTrans or CalcTrans:
reduced = WavRangeReduction(combineDet=combineDet,
out_fit_settings=scale_shift)
except SkipEntry as reason:
#this means that a load step failed, the warning and the fact that the results aren't there is enough for the user
issueWarning(str(reason) + ', skipping entry')
continue
except SkipReduction as reason:
#this means that a load step failed, the warning and the fact that the results aren't there is enough for the user
issueWarning(str(reason) + ', skipping reduction')
continue
except ValueError as reason:
issueWarning('Cannot load file :' + str(reason))
#when we are all up to Python 2.5 replace the duplicated code below with one finally:
delete_workspaces(raw_workspaces)
raise
delete_workspaces(raw_workspaces)
if verbose:
sanslog.notice(
createColetteScript(run, format, reduced, centreit,
plotresults, filename))
# Rename the final workspace
final_name = run['output_as'].strip()
if final_name == '':
final_name = reduced
# Remove illegal characters
final_name = sanitize_name(final_name)
#convert the names from the default one, to the agreement
# This caused a renaming with the following logic
# | combinDet | Name HAB | Name LAB | Name Merged |
# | rear | +_rear | - | - |
# | front | - | +_front | - |
# | both | +_rear | +_front | - |
# | merged | +_rear | +_front | +_merged |
# This is not great since it uses SANS2D terminology for all instruments
names = [final_name]
if combineDet == 'rear':
new_name = su.rename_workspace_correctly(ins_name,
su.ReducedType.LAB,
final_name, reduced)
names = [new_name]
elif combineDet == 'front':
new_name = su.rename_workspace_correctly(ins_name,
su.ReducedType.HAB,
final_name, reduced)
names = [new_name]
elif combineDet == 'both':
if ins_name == 'SANS2D':
rear_reduced = reduced.replace('front', 'rear')
else: #if ins_name == 'lOQ':
rear_reduced = reduced.replace('HAB', 'main')
new_name_HAB = su.rename_workspace_correctly(
ins_name, su.ReducedType.HAB, final_name, reduced)
new_name_LAB = su.rename_workspace_correctly(
ins_name, su.ReducedType.LAB, final_name, rear_reduced)
names = [new_name_HAB, new_name_LAB]
elif combineDet == 'merged':
if ins_name == 'SANS2D':
rear_reduced = reduced.replace('merged', 'rear')
front_reduced = reduced.replace('merged', 'front')
else:
rear_reduced = reduced.replace('merged', 'main')
front_reduced = rear_reduced.replace('main', 'HAB')
new_name_Merged = su.rename_workspace_correctly(
ins_name, su.ReducedType.Merged, final_name, reduced)
new_name_LAB = su.rename_workspace_correctly(
ins_name, su.ReducedType.LAB, final_name, rear_reduced)
new_name_HAB = su.rename_workspace_correctly(
ins_name, su.ReducedType.HAB, final_name, front_reduced)
names = [new_name_Merged, new_name_LAB, new_name_HAB]
else:
RenameWorkspace(InputWorkspace=reduced, OutputWorkspace=final_name)
file = run['output_as']
#saving if optional and doesn't happen if the result workspace is left blank. Is this feature used?
if file:
save_names = []
for n in names:
w = mtd[n]
if isinstance(w, WorkspaceGroup):
save_names.extend(w.getNames())
else:
save_names.append(n)
# If we want to remove zero-errors, we map the original workspace to a cleaned workspace clone,
# else we map it to itself.
save_names_dict = get_mapped_workspaces(save_names,
save_as_zero_error_free)
for algor in list(saveAlgs.keys()):
for workspace_name in save_names:
#add the file extension, important when saving different types of file so they don't over-write each other
ext = saveAlgs[algor]
if not ext.startswith('.'):
ext = '.' + ext
if algor == "SaveCanSAS1D":
# From v2, SaveCanSAS1D is able to save the Transmission workspaces related to the
# reduced data. The name of workspaces of the Transmission are available at the
# sample logs.
_ws = mtd[workspace_name]
transmission_properties = get_transmission_properties(
_ws)
# Add the geometry properties if they exist
if geometry_properties:
transmission_properties.update(geometry_properties)
# Call the SaveCanSAS1D with the Transmission and TransmissionCan if they are
# available
SaveCanSAS1D(save_names_dict[workspace_name],
workspace_name + ext,
DetectorNames=detnames,
**transmission_properties)
elif algor == "SaveNXcanSAS":
_ws = mtd[workspace_name]
transmission_properties = get_transmission_properties(
_ws)
# Call the SaveNXcanSAS with the Transmission and TransmissionCan if they are
# available
SaveNXcanSAS(save_names_dict[workspace_name],
workspace_name + ext,
DetectorNames=detnames,
**transmission_properties)
elif algor == "SaveRKH":
SaveRKH(save_names_dict[workspace_name],
workspace_name + ext,
Append=False)
else:
exec(algor + "('" + save_names_dict[workspace_name] +
"', workspace_name+ext)")
# If we performed a zero-error correction, then we should get rid of the cloned workspaces
if save_as_zero_error_free:
delete_cloned_workspaces(save_names_dict)
if plotresults == 1:
for final_name in names:
PlotResult(final_name)
#the call to WaveRang... killed the reducer so copy back over the settings
ReductionSingleton().replace(copy.deepcopy(local_settings))
ReductionSingleton().settings = local_prop_man_settings.clone(
REDUCTION_SETTINGS_OBJ_NAME)
# Set everything back to the initial state
ReductionSingleton().replace(copy.deepcopy(settings))
ReductionSingleton().settings = prop_man_settings.clone(
REDUCTION_SETTINGS_OBJ_NAME)
#end of reduction of all entries of batch file
return scale_shift
def unixLikePathFromWorkspace(ws):
return su.getFilePathFromWorkspace(ws).replace('\\', '/')
# D_T for nine blocks when dae playing up in cycle 09/1 or 09/2
wksp="SANS2D00001674"
wksp="5976_sans_nxs"
dimdet=192
spec1=8+1+192*192
tag="frt"
#spec1=8+1
#tag="rear"
#print speclist
i=0
namelist=["A TL","D TC","G TR","B ML","E MC","H MR","C BL","F BC","I BR"]
masklist=["h0>h127,v64>v191","h0>h127,v0>v63,v128>v191","h0>h127,v0>v127","h0>h63,h128>h191,v64>v191","h0>h63,h128>h191,v0>v63,v128>v191","h0>h63,h128>h191,v0>v127","h63>h191,v64>v191","h63>h191,v0>v63,v128>v191","h63>h191,v0>v127"]
for name in namelist:
print "i= "+str(i)
# guess "orientation"
list = SANSUtility.ConvertToSpecList(masklist[i], spec1, dimdet,'0')
CropWorkspace(wksp, OutputWorkspace = "D_T "+name+tag, StartWorkspaceIndex=(spec1-1), EndWorkspaceIndex=str(spec1+192*192-2))
SANSUtility.MaskBySpecNumber("D_T "+name+tag, list)
SumSpectra("D_T "+name+tag,"D_T "+name+tag)
i=i+1
print "done"
for wext in namelist:
wsp="D_T "+wext
if wext==namelist[0]:
plot2=plotSpectrum(wsp+tag,0)
layer=plot2.activeLayer()
layer.setTitle("D_T modules")
else:
mergePlots(plot2,plotSpectrum(wsp+tag,0))
layer.setCurveTitle(i,name)
#
def test_empty_string_is_valid(self):
self.checkValues(su.sliceParser(""), [[-1, -1]])
def getCurrSliceLimit(self):
if not self._slices_def:
self._slices_def = su.sliceParser("")
assert self._slice_index == 0
return self._slices_def[self._slice_index]
def setSlicesLimits(self, str_def):
self._slices_def = su.sliceParser(str_def)
self._slice_index = 0
def test_accept_spaces(self):
self.checkValues(su.sliceParser("1 - 2, 3 - 4"), [[1, 2], [3, 4]])
def _match_IDF(self, run):
'''
Compares the IDF in the stored instrument with the IDF in the workspace.
If they are the same all is well. If they diff, then load the adequate
user file.
@param run: name of the run for which the file is to be extracted
'''
# We need the instrument name and the measurement time to determine
# the IDF
measurement_time = None
instrument_name = self.get_instrument_name()
# We need to be able to handle file-based and workspace-based queries
# If we have a workspace we look at the end time, else we
# need a sophisticated extraction mechanism
if isinstance(run, Workspace):
ws = None
if isinstance(run, WorkspaceGroup):
# Just look at the first element in a workspace group
ws = run[0]
else:
ws = run
measurement_time = str(ws.getRun().endTime()).strip()
else:
if run is None or run == "":
return
measurement_time = su.get_measurement_time_from_file(run)
# Get the path to the instrument definition file
idf_path_workspace = ExperimentInfo.getInstrumentFilename(
instrument_name, measurement_time)
idf_path_workspace = os.path.normpath(idf_path_workspace)
# Get the idf from the reducer
idf_path_reducer = self.get_idf_file_path()
idf_path_reducer = os.path.normpath(idf_path_reducer)
# Now check if both idf paths and underlying files. If they are, then don't do anything
# else switch the underlying instrument
if idf_path_reducer == idf_path_workspace and su.are_two_files_identical(
idf_path_reducer, idf_path_reducer):
return
else:
logger.notice("Updating the IDF of the Reducer. Switching from " +
str(idf_path_reducer) + " to " +
str(idf_path_workspace))
idf_path = os.path.basename(idf_path_workspace)
instrument = self._get_correct_instrument(instrument_name,
idf_path)
# Get detector of the old instrument
old_instrument = self.get_instrument()
old_detector_selection = old_instrument.get_detector_selection()
if instrument is not None:
self.set_instrument(instrument)
# We need to update the instrument, by reloading the user file.
# This is pretty bad, but looking at the reducer architecture this
# seems to be the only reasonable way to do this.
self.user_settings.execute(self)
# Now we set the correct detector, this is also being done in the GUI
self.get_instrument().setDetector(old_detector_selection)